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Pierre Nicolas

Contact information

Tel: +33-(0)134652904



Mailing address:
Unité MIG
INRA - Domaine de Vivert
F-78352 Jouy-en-Josas, France

Getting here from Paris by train.



I work as a researcher at the INRA Jouy-en-Josas campus in the Mathématique, Informatique et Génome laboratory (MIG). My interest focuses mainly on statistical bioinformatics with applications to bacterial genome analysis (annotation, population genetics and phylogeny).

Background

Some links

  • SSB A research group in statistics for biology animated by Sophie Schbath.
  • Basysbio A European project I'm involved in.
  • SHOW A powerful self-training bacterial gene detection program (among other things) that I developped during my PhD.
  • A sequencing project that aims at characterizing the evolutionary dynamics of the genus Flavobacterium.

Publications

  • P. Nicolas, A. Leduc, S. Robin, S. Rasmussen, H. Jarmer and P. Bessières. (2009) Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics. 25. 2341-2347 (PubMed). Program and data available here.

  • A. Barinov, V. Loux, A. Hammani, P. Nicolas, P. Langella, SD Ehrlich, E. Maguin and M. van de Guchte. (2009) Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram positive bacteria. Proteomics. 9. 61-73. (PubMed)

  • P. Nicolas, S. Mondot, G. Achaz, C. Bouchenot, J.-F. Bernardet and E. Duchaud. (2008) Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl. Environ. Microbiol. 74. 3702-9 (PubMed). The Flavobacterium psychrophilum MLST database is accessible here.

  • M. Ibrahim, P. Nicolas, P. Bessières, A. Bolotin, V. Monnet and R. Gardan. (2007) A genome-wide survey of short coding sequences in streptococci. Microbiology. 153.3631-44. (PubMed)

  • P. Nicolas, P. Bessières, SD Ehrlich, E. Maguin and M. van de Guchte. (2007) Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract. BMC Evol Biol. 7. 141 (PubMed)

  • E. Duchaud, M. Boussaha, V. Loux, J.-F. Bernardet, C. Michel, B. Kerouault, S. Mondot, P. Nicolas, R. Bossy, C. Caron, P. Bessières, J.-F. Gibrat, S. Claverol, F. Dumetz, M. Le Hénaff and A. Benmansour. (2007) Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nature Biotechnology. 25. 763-9. (PubMed)

  • P. Nicolas, K.M. Kim, D. Shibata and S. Tavaré (2007) The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns. PLoS Computational Biology. 3. e28.(PubMed)

  • K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin, M. Hoebeke, P. Bessières and J-F. Gibrat. (2006) AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 34. 3533--3545. (PubMed)

  • P. Nicolas, F. Sun and L.M. Li. (2006) A model-based approach to selection of tag SNPs. BMC Bioinformatics. 7. 303. (PubMed)

  • M. van de Guchte, S. Penaud, C. Grimaldi, V. Barbe, K. Bryson, P. Nicolas, C. Robert, S. Oztas, S. Mangenot, A. Couloux, V. Loux, R. Dervyn, R. Bossy, A. Bolotin, J.M. Batto, T. Walunas, J.-F. Gibrat, P. Bessières, J. Weissenbach, S.D. Ehrlich and E. Maguin. (2006). The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA. 103. 9274-9. (PubMed)

  • P. Nicolas, A.-S. Tocquet, V. Miele, F. Muri (2006) A reversible jump Markov chain Monte Carlo algorithm for bacterial promoter motifs discovery. J Comput Biol. 13. 651-67. (PubMed)

  • A. Marin, T.E. Malliavin, P. Nicolas, M.A. Delsuc (2004) From NMR chemical shifts to amino acid types: investigation of the predictive power carried by nuclei. J Biomol NMR. 30.47-60. (PubMed)

  • C. Robert, M.-O. Bancal, P. Nicolas, C. Lannou, B. Ney (2004) Analysis and modelling of effects of leaf rust and Septoria tritici blotch on wheat growth. J Exp Bot. 55. 1079-94. (PubMed)

  • M. Hoebeke, P. Nicolas, P. Bessières (2003) MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics. 19. 859-64. (PubMed)

  • K. Marrocco, A. Lecureuil, P. Nicolas, P. Guerche (2003) The Arabidopsis SKP1-like genes present a spectrum of expression profiles. Plant Mol Biol. 52. 715-27. (PubMed)

  • P. Nicolas, L. Bize, F. Muri, M. Hoebeke, F. Rodolphe, S.D. Ehrlich, B. Prum, P. Bessières (2002) Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res. 30. 1418-26. (PubMed)